X-RAY DIFFRACTION Experimental Data & Validation


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Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8
Temperature 298.0
Details 25% polyethylene glycol (PEG) 8000, 0.2 M ammonium sulphate, 0.1 M Tris buffer, pH 8, and 100 mM benzylamine, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 54.21 α = 90
b = 56.66 β = 90
c = 66.13 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2001-06-13
Diffraction Radiation
Monochromator Protocol
Si111 SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-4 0.9763 ESRF ID14-4

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot
1.4 42 99.89 0.047 -- -- 13.4 41043 40997 0.0 -3.0 12.45
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
1.4 1.47 98.3 0.227 0.227 3.6 12.5 --

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
RIP - Radiation-Damage Induced Phasing 1.4 41.89 -- 0.0 40997 40997 2061 99.89 0.13919 0.13919 0.13785 0.16464 RANDOM
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 1.4 1.436 -- 150 2812 0.185 0.232 -- --
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Anisotropic for protein and ligands. Water molecules are refined isotropic
Mean Isotropic B 14.343
Anisotropic B[1][1] -0.1
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.02
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.08
RMS Deviations
Key Refinement Restraint Deviation
r_sphericity_bonded 7.071
r_sphericity_free 1.262
r_rigid_bond_restr 1.263
r_scangle_it 4.5
r_bond_refined_d 0.016
r_angle_refined_deg 1.626
r_dihedral_angle_1_deg 6.386
r_chiral_restr 0.123
r_gen_planes_refined 0.009
r_nbd_refined 0.198
r_xyhbond_nbd_refined 0.123
r_symmetry_vdw_refined 0.165
r_symmetry_hbond_refined 0.147
r_mcbond_it 1.608
r_mcangle_it 2.566
r_scbond_it 3.388
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1629
Nucleic Acid Atoms 0
Heterogen Atoms 25
Solvent Atoms 288

Software

Computing
Computing Package Purpose
PRODC Data Reduction (intensity integration)
CCP4 (SCALA) Data Reduction (data scaling)
SHELXD, SHARP Structure Solution
REFMAC 5.1.24 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.1.24 refinement
sharp model building
shelxd model building
SCALA data reduction
prodc data collection